Biology subjects

Wang, K.

Publications and source records attributed to Wang, K..

At least 415 records · Page 23Linked to original sources

bioRxiv2020

Single-cell multi-omics reveals elevated plasticity and stem-cell-like blasts relevant to the poor prognosis of KMT2A-rearranged leukemia

Infant ALL is a devastating malignancy caused by rearrangements of the KMT2A gene (KMT2A-r) in approximately 70% of patients. The outcome is dismal and younger age at diagnosis is associated with increased risk of relapse. To discover age-specific differences and critical drivers that mediate the poor outcome in KMT2A-r ALL, we subjected KMT2A-r leukemias and normal hematopoietic cells from patients of different ages to multi-omic single cell analysis using scRNA-Seq, scATAC-Seq and snmC-Seq2. We uncovered the following critical new insights: Leukemia cells from infants younger than 6 months have a greatly increased lineage plasticity and contain a hematopoietic stem and progenitor-like (HSPC-like) population compared to older infants. We identified an immunosuppressive signaling circuit between the HSPC-like blasts and cytotoxic lymphocytes in younger patients. Both observations offer a compelling explanation for the ability of leukemias in young infants to evade chemotherapy and immune mediated control. Our analysis also revealed pre-existing lymphomyeloid primed progenitor and myeloid blasts at initial diagnosis of B-ALL. Tracking of leukemic clones in two patients whose leukemia underwent a lineage switch documented the evolution of such clones into frank AML. These findings provide critical insights into KMT2A-r ALL and have potential clinical implications for targeted inhibitors or multi-target immunotherapy approaches. Beyond infant ALL, our study demonstrates the power of single cell multi-omics to detect tumor intrinsic and extrinsic factors affecting rare but critical subpopulations within a malignant population that ultimately determines patient outcome.

cancer biology↗

bioRxiv2020

Independent parental contributions initiate zygote polarization in Arabidopsis thaliana

Embryogenesis of flowering plants is initiated by polarization of the zygote, a prerequisite for correct axis formation in the embryo. Zygote polarity and the decision between embryonic and non-embryonic development in the daughter cells is controlled by a MITOGEN-ACTIVATING PROTEIN (MAP) kinase signaling pathway including the MAPKK kinase YODA (YDA). Upstream of YDA act two members of the BRASINOSTEROID SIGNALING KINASE (BSK) family, BSK1 and BSK2. These membrane-associated proteins serve as signaling relay linking receptor kinase complexes with intracellular signaling cascades. The receptor kinases acting upstream of BSK1 and BSK2 in the zygote, however, have so far not been identified. Instead, YDA can in part be activated by the non-canonical BSK family member SHORT SUSPENSOR (SSP) that is contributed by the sperm cell during fertilization. Here, we show that the receptor kinase ERECTA plays a crucial role in zygote polarization as maternally contributed part of the embryonic YDA pathway. SSP on the other hand provides an independent, paternal input to YDA activation, outlining a Y-shaped pathway. We conclude that two independent parental contributions initiate zygote polarization and control suspensor formation and embryonic development.

plant biology↗

bioRxiv2020

LncRNA H19X is required for placenta development and angiogenesis through regulating a noncoding RNA regulatory network

H19X is a lncRNA specifically expressed in the placenta, whose expression is induced by hypoxia. H19X overexpression promoted trophoblast proliferation and invasion, while its knockdown or knockout inhibited trophoblast proliferation and invasion. Mechanistically, we demonstrated that reciprocal regulation exists with miR-424/miR-503 in the control of genes related to placental development and angiogenesis, including VEGF and VEGFR2. H19X inhibited ubiquitination of PIWIL1, thereby maintaining its stability and homeostatic expression of piRNAs. PIWIL1 overexpression rescued the defects of cell behavior caused by H19X KO. H19X deletion led to compromised HIF-1A/HIF-2A expression, which was correlated with the dysregulation of downstream genes under hypoxic conditions. CRISPR/Cas-9 knockout of H19X in animals led to defective placenta differentiation and compromised embryo development under hypoxic conditions. Western blotting showed reduced expression levels of PIWIL1 as well as angiogenesis marker genes, including VEGF and VEGFR2, in H19X KO mice. Thus, this study provides evidence of an unexpected link among lncRNA, miRNA, PIWIL1-related piRNA, and angiogenesis in placentation, the dysregulation of which leads to poor placental development and embryo loss under hypoxic conditions.

developmental biology↗

bioRxiv2020

NERO: A Biomedical Named-entity (Recognition) Ontology with a Large, Annotated Corpus Reveals Meaningful Associations Through Text Embedding

Machine reading is essential for unlocking valuable knowledge contained in the millions of existing biomedical documents. Over the last two decades 1,2, the most dramatic advances in machine-reading have followed in the wake of critical corpus development3. Large, well-annotated corpora have been associated with punctuated advances in machine reading methodology and automated knowledge extraction systems in the same way that ImageNet 4 was fundamental for developing machine vision techniques. This study contributes six components to an advanced, named-entity analysis tool for biomedicine: (a) a new, Named-Entity Recognition Ontology (NERO) developed specifically for describing entities in biomedical texts, which accounts for diverse levels of ambiguity, bridging the scientific sublanguages of molecular biology, genetics, biochemistry, and medicine; (b) detailed guidelines for human experts annotating hundreds of named-entity classes; (c) pictographs for all named entities, to simplify the burden of annotation for curators; (d) an original, annotated corpus comprising 35,865 sentences, which encapsulate 190,679 named entities and 43,438 events connecting two or more entities; (e) validated, off-the-shelf, named-entity recognition automated extraction, and; (f) embedding models that demonstrate the promise of biomedical associations embedded within this corpus.

systems biology↗

bioRxiv2020

Study on H3K9 acetylation modification and TLR9 immune regulation mechanism in patients with anti-HBV treatment using thymosin a1 combined with entecavir

For hepatitis B antiviral treatment, there has been no comprehensive method yet. Interferon has poor antiviral efficacy, while nucleoside drugs have long course of treatment and high relapse rate. To improve the anti-HBV curative effect, treatment methods such as thymosin combined with entecavir have become a focus of clinical investigation. To explore potential mechanism of the combination therapy, based on previous studies, this paper explores the relationship between TLR9 expression in PBMCs, secretion of corresponding downstream inflammatory factors and HBV load in anti-HBV treatment with Thymosin a1 (Ta1) combined with entecavir. Chromatin immunoprecipitation combined with PCR method was adopted to detect H3K9 acetylation modification in patients. The relationship between TLR9 expression was explored using RT-QPCR, the relationship between secretion of inflammatory factors, efficacy and TLR9 mRNA expression was determined using Luminex technology. The results showed that during anti-HBV treatment with Ta1 combined with entecavir, histone acetylation increased in patients PBMCs, acetylated protein H3K9Ac had significant binding with promoter region of the TRL9 gene, thereby increasing the expression of TRL9 mRNA, activating the immune pathway under TRL9 regulation, promoting secretion of inflammation factors IL-6, IL-12, IFN-{gamma}, and TNF-, boosting the progress of antiviral therapy. H3K9 acetylation modification of TLR9 exists and plays an important role in patients with chronic hepatitis B. During the combination therapy with entecavir and Ta1, histone acetylation modification of TLR9 was significantly improved, which increased the expression of TLR9 at the mRNA and protein levels, and further regulated IL-6, IL-12 and other cytokines.

pharmacology and toxicology↗

bioRxiv2020

Spatially expandable fiber-based probes as a multifunctional deep brain interface

Understanding the cytoarchitecture and wiring of the brain requires improved methods to record and stimulate large groups of neurons with cellular specificity. This requires miniaturized neural interfaces that integrate into brain tissue without altering its properties. Existing neural interface technologies have been shown to provide high-resolution electrophysiological recording with high signal-to-noise ratio. However, with single implantation, the physical properties of these devices limit their access to one, small brain region. To overcome this limitation, we developed a platform that provides three-dimensional coverage of brain tissue through multisite multifunctional fiber-based neural probes guided in a helical scaffold. Chronic recordings from the spatially expandable fiber probes demonstrate the ability of these fiber probes capturing brain activities with a single-unit resolution for long observation times. Furthermore, using Thy1-ChR2-YFP mice we demonstrate the application of our probes in simultaneous recording and optical/chemical modulation of brain activities across distant regions. Similarly, varying electrographic brain activities from different brain regions were detected by our customizable probes in a mouse model of epilepsy, suggesting the potential of using these probes for the investigation of brain disorders such as epilepsy. Ultimately, this technique enables three-dimensional manipulation and mapping of brain activities across distant regions in the deep brain with minimal tissue damage, which can bring new insights for deciphering complex brain functions and dynamics in the near future.

bioengineering↗

bioRxiv2020

Reverse-transcription recombinase-aided amplification assay for H5 subtype avian influenza virus

The H5 subtype Avian Influenza Virus has caused huge economic losses to the poultry industry and is a threat to human health. A rapid and simple test is needed to confirm infection in suspected cases during disease outbreaks. In this study, we developed a reverse-transcription recombinase-aided amplification assay for the detection of H5 subtype avian influenza virus. Assays were performed at a single temperature (39{degrees}C), and the results were obtained within 20 min. The assay showed no cross-detection with Newcastle disease virus or infectious bronchitis virus. The analytical sensitivity was 103 RNA copies per reaction at a 95% confidence interval according to probit regression analysis, with 100% specificity. Compared with published reverse-transcription quantitative real-time polymerase chain reaction assays, the {kappa} value of the reverse transcription recombinase-aided amplification assay in 365 avian clinical samples was 0.970 (p < 0.001). The sensitivity for avian clinical sample detection was 94.44% (95%CI, 70.63% - 99.71%), and the specificity was 100% (95%CI, 98.64% - 100%). These results indicated that our reverse-transcription recombinase-aided amplification assay may be a valuable tool for detecting H5 subtype avian influenza virus.

molecular biology↗

bioRxiv2020

Structural and biochemical characterization of bifunctional XynA

Xylan and cellulose are the two major constituents in numerous types of lignocellulosic biomass, representing a promising resource for biofuels and other biobased industries. The efficient degradation of lignocellulose requires the synergistic actions of cellulase and xylanase. Thus, bifunctional enzyme incorporated xylanase/cellulase activity has attracted considerable attention since it has great cost savings potential. Recently, a novel GH10 family enzyme XynA identified from Bacillus sp. is found to degrade both cellulose and xylan. To understand its molecular catalytic mechanism, here we first solve the crystal structure of XynA at 2.3 [A]. XynA is characterized with a classic (/{beta})8 TIM-barrel fold (GH10 domain) flanked by the flexible N-terminal domain and C-terminal domain. Circular dichroism, protein thermal shift and enzyme activity assays reveal that conserved residues Glu182 and Glu280 are both important for catalytic activities of XynA, which is verified by the crystal structure of XynA with E182A/E280A double mutant. Molecular docking studies of XynA with xylohexaose and cellohexaose as well as site-directed mutagenesis and enzyme activity assay demonstrat that Gln250 and His252 are indispensible to cellulase and bifunctional activity, separately. These results elucidate the structural and biochemical features of XynA, providing clues for further modification of XynA for industrial application.

molecular biology↗

bioRxiv2020

Somatosensory evoked potentials indexing lateral inhibition are modulated according to the mode of perceptual processing: comparing or combining multi-digit tactile motion

Many perceptual studies focus on the brains capacity to discriminate between stimuli. However, our normal experience of the world also involves integrating multiple stimuli into a single perceptual event. Neural circuit mechanisms such as lateral inhibition are believed to enhance local differences between sensory inputs from nearby regions of the receptor surface. However, this mechanism would seem dysfunctional when sensory inputs need to be combined rather than contrasted. Here, we investigated whether the brain can strategically regulate the strength of suppressive interactions that underlie lateral inhibition between finger representations in human somatosensory processing. To do this, we compared sensory processing between conditions that required either comparing or combining information. We delivered two simultaneous tactile motion trajectories to index and middle fingertips of the right hand. Participants had to either compare the directions of the two stimuli, or to combine them to form their average direction. To reveal preparatory tuning of somatosensory cortex, we used an established event-related potential design to measure the interaction between cortical representations evoked by digital nerve shocks immediately before each tactile stimulus. Consistent with previous studies, we found a clear suppressive interaction between cortical activations when participants were instructed to compare the tactile motion directions. Importantly, this suppressive interaction was significantly reduced when participants had to combine the same stimuli. These findings suggest that the brain can strategically switch between a comparative and a combinative mode of somatosensory processing, according to the perceptual goal, by preparatorily adjusting the strength of a process akin to lateral inhibition.

neuroscience↗

bioRxiv2020

The genomic formation of First American ancestors in East and Northeast Asia

Upward Sun River 1, an individual from a unique burial of the Denali tradition in Alaska (11500 calBP), is considered a type representative of Ancient Beringians who split from other First Americans 22000-18000 calBP in Beringia. Using a new admixture graph model-comparison approach resistant to overfitting, we show that Ancient Beringians do not form the deepest American lineage, but instead harbor ancestry from a lineage more closely related to northern North Americans than to southern North Americans. Ancient Beringians also harbor substantial admixture from a lineage that did not contribute to other Native Americans: Amur River Basin populations represented by a newly reported site in northeastern China. Relying on these results, we propose a new model for the genomic formation of First American ancestors in Asia. One Sentence SummaryAncient Beringians do not form the deepest American lineage, but harbor admixture from Amur River Basin populations.

genetics↗

bioRxiv2020

CancerVar: a web server for improved evidence-based clinical interpretation of cancer somatic mutations and copy number abnormalities

Several knowledgebases, such as CIViC and OncoKB, have been manually curated to support clinical interpretations of a limited number of "hotspot" somatic mutations in cancer, yet discrepancies or even conflicting interpretations have been observed among these knowledgebases. Additionally, while these knowledgebases have been extremely useful, they typically cannot interpret novel mutations, which may also have functional and clinical impacts in cancer. To address these challenges, we developed an automated interpretation tool called CancerVar (Cancer Variants interpretation) to score more than 12.9 million somatic mutations and classify them into four tiers: strong clinical significance, potential clinical significance, uncertain clinical significance, and benign/likely benign, based on the AMP/ASCO/CAP 2017 guideline. Considering that the AMP/ASCO/CAP rule-based scoring system may have inherent limitations, such as lack of a clear guidance on weighing different pieces of functional evidence or unclear definition for certain clinical evidence, it may cause misinterpretation for certain variants that have functional impacts but no proven clinical significance. To address this issue, we further introduced a deep learning-based scoring system to predict oncogenicity of mutations by semi-supervised generative adversarial network (SGAN) method using both functional and clinical evidence. We trained and validated the SGAN model on 5,234 somatic mutations from an in-house database of clinical reports on cancer patients, and achieved a good performance when testing on 6,226 variants that were curated by us through literature search. We also compared the prediction with several independent datasets and showed great utility in classifying variants with previously unknown interpretations. CancerVar is also incorporated into a web server that can generate automated texts with summarized descriptive interpretations, such as diagnostic, prognostic, targeted drug responses and clinical trial information for many hotspot mutations. In summary, CancerVar can facilitate clinical interpretation and hypothesis generation for somatic mutations, and greatly reduce manual workload for retrieving relevant evidence and implementing existing guidelines.

cancer biology↗

bioRxiv2020

A Joint Deep Learning Model for Simultaneous Batch Effect Correction, Denoising and Clustering in Single-Cell Transcriptomics

Recent development of single-cell RNA-seq (scRNA-seq) technologies has led to enormous biological discoveries. As the scale of scRNA-seq studies increases, a major challenge in analysis is batch effect, which is inevitable in studies involving human tissues. Most existing methods remove batch effect in a low-dimensional embedding space. Although useful for clustering, batch effect is still present in the gene expression space, leaving downstream gene-level analysis susceptible to batch effect. Recent studies have shown that batch effect correction in the gene expression space is much harder than in the embedding space. Popular methods such as Seurat3.0 rely on the mutual nearest neighbor (MNN) approach to remove batch effect in the gene expression space, but MNN can only analyze two batches at a time and it becomes computationally infeasible when the number of batches is large. Here we present CarDEC, a joint deep learning model that simultaneously clusters and denoises scRNA-seq data, while correcting batch effect both in the embedding and the gene expression space. Comprehensive evaluations spanning different species and tissues showed that CarDEC consistently outperforms scVI, DCA, and MNN. With CarDEC denoising, those non-highly variable genes offer as much signal for clustering as the highly variable genes, suggesting that CarDEC substantially boosted information content in scRNA-seq. We also showed that trajectory analysis using CarDECs denoised and batch corrected expression as input revealed marker genes and transcription factors that are otherwise obscured in the presence of batch effect. CarDEC is computationally fast, making it a desirable tool for large-scale scRNA-seq studies.

bioinformatics↗

bioRxiv2020

Reduction of visual stimulus artifacts using a spherical tank for small, aquatic animals

Delivering appropriate stimuli remains a challenge in vision research, particularly for aquatic animals such as zebrafish. Due to the shape of the water tank and the associated optical paths of light rays, the stimulus can be subject to unwanted refraction or reflection artifacts, which may spoil the experiment and result in wrong conclusions. Here, we employ computer graphics simulations and calcium imaging in the zebrafish optic tectum to show, how a spherical glass container optically outperforms many previously used water containers, including Petri dish lids. We demonstrate that aquatic vision experiments suffering from total internal reflection artifacts at the water surface or at the flat container bottom may result in the erroneous detection of visual neurons with bipartite receptive fields and in the apparent absence of neurons selective for vertical motion. Our results and demonstrations will help aquatic vision neuroscientists on optimizing their stimulation setups.

neuroscience↗

bioRxiv2020

1RS.1BL molecular resolution provides novel contributions to wheat improvement

Wheat-rye 1RS.1BL translocation has a significant impact on wheat yield and hence food production globally. However, the genomic basis of its contributions to wheat improvement is undetermined. Here, we generated a high-quality assembly of 1RS.1BL translocation comprising 748,715,293 bp with 4,996 predicted protein-coding genes. We found the size of 1RS is larger than 1BS with the active centromere domains shifted to the 1RS side instead of the 1BL side in Aikang58 (AK58). The gene alignment showed excellent synteny with 1BS from wheat and genes from 1RS were expressed well in wheat especially for 1RS where expression was higher than that of 1BS for the grain-20DPA stage associated with greater grain weight and negative flour quality attributes. A formin-like-domain protein FH14 (TraesAK58CH1B01G010700) was important in regulating cell division. Two PPR genes were most likely the genes for the multi fertility restoration locus Rf multi. Our data not only provide the high-resolution structure and gene complement for the 1RS.1BL translocation, but also defined targets for enhancing grain yield, biotic and abiotic stress, and fertility restoration in wheat.

genomics↗

bioRxiv2020

A key linear epitope for a potent neutralizing antibody to SARS-CoV-2 S-RBD

The spread of SARS-CoV-2 confers a serious threat to the public health without effective intervention strategies1-3. Its variant carrying mutated Spike (S) protein D614G (SD614G) has become the most prevalent form in the current global pandemic4,5. We have identified a large panel of potential neutralizing antibodies (NAbs) targeting the receptor-binding domain (RBD) of SARS-CoV-2 S6. Here, we focused on the top 20 potential NAbs for the mechanism study. Of them, the top 4 NAbs could individually neutralize both authentic SARS-CoV-2 and SD614G pseudovirus efficiently. Our epitope mapping revealed that 16/20 potent NAbs overlapped the same steric epitope. Excitingly, we found that one of these potent NAbs (58G6) exclusively bound to a linear epitope on S-RBD (termed as 58G6e), and the interaction of 58G6e and the recombinant ACE2 could be blocked by 58G6. We confirmed that 58G6e represented a key site of vulnerability on S-RBD and it could positively react with COVID-19 convalescent patients plasma. We are the first, as far as we know, to provide direct evidences of a linear epitope that can be recognized by a potent NAb against SARS-CoV-2 S-RBD. This study paves the way for the applications of these NAbs and the potential safe and effective vaccine design.

immunology↗

bioRxiv2020

LIQA: Long-read Isoform Quantification and Analysis

Long-read RNA sequencing (RNA-seq) technologies have made it possible to sequence full-length transcripts, facilitating the exploration of isoform-specific gene expression (isoform relative abundance and isoform-level TPM) over conventional short-read RNA-seq. However, long-read RNA-seq suffers from high per-base error rate, presence of chimeric reads or alternative alignments, and other biases, which require different analysis methods than short-read RNA-seq. Here we present LIQA (Long-read Isoform Quantification and Analysis), an Expectation-Maximization based statistical method to quantify isoform expression and detect differential alternative splicing (DAS) events using long-read RNA-seq data. Rather than summarizing isoform-specific read counts directly as done in short-read methods, LIQA incorporates base-pair quality score and isoform-specific read length information to assign different weights across reads, which reflects alignment confidence. Moreover, LIQA can detect DAS events between conditions using isoform usage estimates. We evaluated LIQAs performance on simulated data and demonstrated that it outperforms other approaches in characterizing isoforms with low read coverage and in detecting DAS events between two groups. We also generated one direct mRNA sequencing dataset and one cDNA sequencing dataset using the Oxford Nanopore long-read platform, both with paired short-read RNA-seq data and qPCR data on selected genes, and we demonstrated that LIQA performs well in isoform discovery and quantification. Finally, we evaluated LIQA on a PacBio dataset on esophageal squamous epithelial cells, and demonstrated that LIQA recovered DAS events that failed to be detected in short-read data. In summary, LIQA leverages the power of long-read RNA-seq and achieves higher accuracy in estimating isoform abundance than existing approaches, especially for isoforms with low coverage and biased read distribution. LIQA is freely available at https://github.com/WGLab/LIQA.

bioinformatics↗

bioRxiv2020

Celastrol directly inhibits PFKM to induce weight loss and leptin sensitization

Despite the prevalence of obesity and related health consequences around the globe, effective treatments for inducing healthy weight loss are still lacking. Celastrol is a pentacyclic triterpene that was recently identified as a potent anti-obesity agent. Celastrol increases sensitivity to leptin, but the molecular target of celastrol is unknown. Therefore, the mechanisms by which this agent exerts its anti-obesity effect remain elusive. Using tissue-specific ABPP (activity-based protein profiling), we found that PFKM, a rate-limiting enzyme for glycolysis in skeletal muscle, is a direct target of celastrol. Celastrol inhibited PFKM enzymatic activity, and Pfkm knockout mice were resistant to a high fat diet, were hypersensitive to exogenous leptin, and were unresponsive to celastrol. PFKM inhibition led to activation of AMPK and inactivation of ACC in cultured myotubes and mouse skeletal muscle. Specific loss of AMPK in muscle significantly attenuated the anti-obesity effects of celastrol. Further, PFKM inhibition and subsequent activation of the AMPK/ACC signaling pathway reduced levels of free fatty acids by switching energy expenditure and consequently decreasing levels of SOCS1 expression, which are both required for leptin sensitization in 293t/hLepRb cells and mice. Finally, using a high throughput compound screen we identified an alternative PFKM inhibitor, 3-79, which exhibits a strong anti-obesity effect and non-covalent binding capacity. This compound is a promising agent for treating obesity in the clinic.

physiology↗

bioRxiv2020

Generation of thymidine auxotrophic Agrobacterium tumefaciens strains for plant transformation

Agrobacterium-mediated transformation is a widely used gene delivery method for fundamental researches and crop trait improvement projects. Auxotrophic Agrobacterium tumefaciens strains are highly desirable for plant transformation because they can be easily removed from the explants after co-cultivation due to their dependence on essential nutrient supplementation. The thymidine auxotrophic A. tumefaciens strain LBA4404Thy- has been successfully used for plant transformation, however, auxotrophic version of other commonly used strains are not available yet to public laboratories. Here we report the generation of EHA101, EHA105 and EHA105D thymidine auxotrophic strains. These strains exhibited thymidine-dependent growth in the bacterial medium, and the transient GUS expression assay using Arabidopsis seedling showed that they retain the equivalent T-DNA transfer capability as the original strains thus are suitable for plant transformation.

plant biology↗